Literature DB >> 16051588

Phylogenetic diversity and the greedy algorithm.

Mike Steel1.   

Abstract

Given a phylogenetic tree with leaves labeled by a collection of species, and with weighted edges, the "phylogenetic diversity" of any subset of the species is the sum of the edge weights of the minimal subtree connecting the species. This measure is relevant in biodiversity conservation where one may wish to compare different subsets of species according to how much evolutionary variation they encompass. In this note we show that phylogenetic diversity has an attractive mathematical property that ensures that we can solve the following problem easily by the greedy algorithm: find a subset of the species of any given size k of maximal phylogenetic diversity. We also describe an extension of this result that also allows weights to be assigned to species.

Mesh:

Year:  2005        PMID: 16051588     DOI: 10.1080/10635150590947023

Source DB:  PubMed          Journal:  Syst Biol        ISSN: 1063-5157            Impact factor:   15.683


  23 in total

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4.  Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems.

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5.  Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity.

Authors:  Binh Nguyen; Andreas Spillner; Brent C Emerson; Vincent Moulton
Journal:  Algorithms Mol Biol       Date:  2010-03-20       Impact factor: 1.405

6.  Choosing Subsamples for Sequencing Studies by Minimizing the Average Distance to the Closest Leaf.

Authors:  Jonathan T L Kang; Peng Zhang; Sebastian Zöllner; Noah A Rosenberg
Journal:  Genetics       Date:  2015-08-24       Impact factor: 4.562

7.  Surprising results on phylogenetic tree building methods based on molecular sequences.

Authors:  Gaston H Gonnet
Journal:  BMC Bioinformatics       Date:  2012-06-27       Impact factor: 3.169

8.  A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade.

Authors:  Björn Brindefalk; Thijs J G Ettema; Johan Viklund; Mikael Thollesson; Siv G E Andersson
Journal:  PLoS One       Date:  2011-09-14       Impact factor: 3.240

9.  A simple, fast, and accurate method of phylogenomic inference.

Authors:  Martin Wu; Jonathan A Eisen
Journal:  Genome Biol       Date:  2008-10-13       Impact factor: 13.583

10.  Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.

Authors:  Jenna Morgan Lang; Aaron E Darling; Jonathan A Eisen
Journal:  PLoS One       Date:  2013-04-25       Impact factor: 3.240

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